February 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 0496cd: Update Test
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0496cda46ed0c0800859654a87a4405a0cc83eac https://github.com/galaxyproject/usegalaxy-playbook/commit/0496cda46ed0c080… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 0b4058b85985fc6a0a5127f15f5e2c85bd657c23 https://github.com/galaxyproject/usegalaxy-playbook/commit/0b4058b85985fc6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: A env/common/client.yml A env/test/client.yml A env/test/group_vars/cvmfsstratum0servers.yml A roles/usegalaxy_cvmfs/tasks/_inc_client_build.yml A roles/usegalaxy_cvmfs/tasks/client.yml M roles/usegalaxy_cvmfs/tasks/main.yml M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- Add client building for Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0a1fada824cf...…

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[galaxyproject/galaxy] 2f020e: Fix tool stdio level parsing for OOM level.
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2f020ef9441d3eec8f0d517fe9f3412df1bfb8d5 https://github.com/galaxyproject/galaxy/commit/2f020ef9441d3eec8f0d517fe9f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Fix tool stdio level parsing for OOM level. Backend was enhanced to allow this in #5196 and a new entry point to setting exit code for such exit conditions but the custom parsing wasn't updated to allow it. Thanks to @nsoranzo for the catch. Commit: c3ada7f16973718f49ffeb1de8dc44f882ee9fd2 https://github.com/galaxyproject/galaxy/commit/c3ada7f16973718f49ffeb1de8dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #5460 from jmchilton/fix_oom_parse [18.01] Fix tool stdio level parsing for OOM level. Compare: https://github.com/galaxyproject/galaxy/compare/f0a8243f7d40...c3ada7f16973

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[galaxyproject/galaxy] ab3d53: More options for collection deletion.
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab3d53c5ce170855d68c955f5cb453d70989f630 https://github.com/galaxyproject/galaxy/commit/ab3d53c5ce170855d68c955f5cb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- More options for collection deletion. Delete button now a drop down menu (like dropdown for downloading metadata files). - Top option just deletes the collection. - Second option deletes the collection and attempts to delete the datasets contained within it. - The third option deletes the collection and attempts to purge the datasets within it. Commit: b0162ba5431097185faf641935d6ca27e11073e2 https://github.com/galaxyproject/galaxy/commit/b0162ba5431097185faf641935d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/util/facts.py Log Message: ----------- Fix server_name when config is a dict. Commit: 55b6d601a8ae5ad43a234721b2b21cc6db6ae067 https://github.com/galaxyproject/galaxy/commit/55b6d601a8ae5ad43a234721b2b2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- add empty href to links so the cursor is right Commit: 8019afb8b544ef57de953d8ae23e8a45b0e15d52 https://github.com/galaxyproject/galaxy/commit/8019afb8b544ef57de953d8ae23e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- fix typo Commit: 3512096a146f7d32ebc352049717df22a7c87fef https://github.com/galaxyproject/galaxy/commit/3512096a146f7d32ebc352049717… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- remove unused classes and aria Commit: dac1ba58124eb0d3b96cf6e114f6ff0e101726c8 https://github.com/galaxyproject/galaxy/commit/dac1ba58124eb0d3b96cf6e114f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix failing integration tests for workflow handlers. Commit: b28fb7e4d7af29ffd6db7ce2674fe2be3d6dad03 https://github.com/galaxyproject/galaxy/commit/b28fb7e4d7af29ffd6db7ce2674f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M client/galaxy/style/less/ui/icon-btn.less Log Message: ----------- change the history icon-btn selector to work with dropdowns Commit: 2cb3af5d60d5fe08889691a8ff3b2b31038727b7 https://github.com/galaxyproject/galaxy/commit/2cb3af5d60d5fe08889691a8ff3b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py Log Message: ----------- Merge pull request #5447 from natefoo/server-name-fix [18.01] Fix server_name when config is a dict Commit: 0704d63d0b6353cf59153f59ab27519dc6bfc7d4 https://github.com/galaxyproject/galaxy/commit/0704d63d0b6353cf59153f59ab27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/less/ui/icon-btn.less M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01 Commit: f0a8243f7d4079ac406e0a2d8b0a061f1745dca1 https://github.com/galaxyproject/galaxy/commit/f0a8243f7d4079ac406e0a2d8b0a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Client-format post-merge Commit: 3a7414acaca59dc602ab3ea8092df2be9ce34258 https://github.com/galaxyproject/galaxy/commit/3a7414acaca59dc602ab3ea8092d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/less/ui/icon-btn.less M lib/galaxy/config.py M lib/galaxy/managers/collections.py M lib/galaxy/util/facts.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/490f67f3a0e7...3a7414acaca5

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[galaxyproject/galaxy] ab3d53: More options for collection deletion.
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ab3d53c5ce170855d68c955f5cb453d70989f630 https://github.com/galaxyproject/galaxy/commit/ab3d53c5ce170855d68c955f5cb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- More options for collection deletion. Delete button now a drop down menu (like dropdown for downloading metadata files). - Top option just deletes the collection. - Second option deletes the collection and attempts to delete the datasets contained within it. - The third option deletes the collection and attempts to purge the datasets within it. Commit: 55b6d601a8ae5ad43a234721b2b21cc6db6ae067 https://github.com/galaxyproject/galaxy/commit/55b6d601a8ae5ad43a234721b2b2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- add empty href to links so the cursor is right Commit: 8019afb8b544ef57de953d8ae23e8a45b0e15d52 https://github.com/galaxyproject/galaxy/commit/8019afb8b544ef57de953d8ae23e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- fix typo Commit: 3512096a146f7d32ebc352049717df22a7c87fef https://github.com/galaxyproject/galaxy/commit/3512096a146f7d32ebc352049717… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- remove unused classes and aria Commit: b28fb7e4d7af29ffd6db7ce2674fe2be3d6dad03 https://github.com/galaxyproject/galaxy/commit/b28fb7e4d7af29ffd6db7ce2674f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M client/galaxy/style/less/ui/icon-btn.less Log Message: ----------- change the history icon-btn selector to work with dropdowns Commit: 0704d63d0b6353cf59153f59ab27519dc6bfc7d4 https://github.com/galaxyproject/galaxy/commit/0704d63d0b6353cf59153f59ab27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/less/ui/icon-btn.less M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01 Commit: f0a8243f7d4079ac406e0a2d8b0a061f1745dca1 https://github.com/galaxyproject/galaxy/commit/f0a8243f7d4079ac406e0a2d8b0a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Client-format post-merge Compare: https://github.com/galaxyproject/galaxy/compare/2cb3af5d60d5...f0a8243f7d40

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[galaxyproject/galaxy] 4347d5: Pass query params separately to visit_url() and vi...
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4347d5f83debc78a86c6be2fc4809cd99714124b https://github.com/galaxyproject/galaxy/commit/4347d5f83debc78a86c6be2fc480… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Pass query params separately to visit_url() and visit_galaxy_url() For proper encoding. Commit: 490f67f3a0e70f9d90898163ea42e7d273c790ba https://github.com/galaxyproject/galaxy/commit/490f67f3a0e70f9d90898163ea42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #5458 from nsoranzo/ts_tests_query_params Pass query params separately to visit_url() and visit_galaxy_url() Compare: https://github.com/galaxyproject/galaxy/compare/204bb0e8fdf5...490f67f3a0e7

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[galaxyproject/infrastructure-playbook] b27e8c: More stdout/stderr handling for spartbalance
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b27e8c6159fe40c52870b5eeba8c463256e8de45 https://github.com/galaxyproject/infrastructure-playbook/commit/b27e8c6159f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M taccenv/files/slurm/spartbalance Log Message: ----------- More stdout/stderr handling for spartbalance

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[galaxyproject/galaxy] b0162b: Fix server_name when config is a dict.
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b0162ba5431097185faf641935d6ca27e11073e2 https://github.com/galaxyproject/galaxy/commit/b0162ba5431097185faf641935d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/util/facts.py Log Message: ----------- Fix server_name when config is a dict. Commit: dac1ba58124eb0d3b96cf6e114f6ff0e101726c8 https://github.com/galaxyproject/galaxy/commit/dac1ba58124eb0d3b96cf6e114f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix failing integration tests for workflow handlers. Commit: 2cb3af5d60d5fe08889691a8ff3b2b31038727b7 https://github.com/galaxyproject/galaxy/commit/2cb3af5d60d5fe08889691a8ff3b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py Log Message: ----------- Merge pull request #5447 from natefoo/server-name-fix [18.01] Fix server_name when config is a dict Compare: https://github.com/galaxyproject/galaxy/compare/207f5faba0ab...2cb3af5d60d5

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[galaxyproject/galaxy] 5958d1: Remove static/scripts/* from the dev branch, add t...
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5958d173c44e20e8860f90498f01cf2e6f510cf9 https://github.com/galaxyproject/galaxy/commit/5958d173c44e20e8860f90498f01… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M .gitignore R static/scripts/admin.toolshed.js R static/scripts/bundled/admin.bundled.js R static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/extended.bundled.js R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/login.bundled.js R static/scripts/galaxy.interactive_environments.js R static/scripts/galaxy.js R static/scripts/galaxy.library.js R static/scripts/galaxy.pages.js R static/scripts/i18n.js R static/scripts/layout/generic-nav-view.js R static/scripts/layout/masthead.js R static/scripts/layout/menu.js R static/scripts/layout/modal.js R static/scripts/layout/page.js R static/scripts/layout/panel.js R static/scripts/layout/router.js R static/scripts/layout/scratchbook.js R static/scripts/legacy/grid/grid-model.js R static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R static/scripts/libs/jquery/jquery.migrate.js R static/scripts/libs/jquery/jquery.mousewheel.js R static/scripts/libs/jquery/jquery.rating.js R static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/jquery/jstorage.js R static/scripts/libs/jquery/jstree.js R static/scripts/libs/jquery/select2.js R static/scripts/libs/raven.js R static/scripts/libs/require.js R static/scripts/libs/toastr.js R static/scripts/libs/underscore.js R static/scripts/mvc/annotation.js R static/scripts/mvc/base-mvc.js R static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/collection/base-creator.js R static/scripts/mvc/collection/collection-li-edit.js R static/scripts/mvc/collection/collection-li.js R static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-view-edit.js R static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/collection/list-collection-creator.js R static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/dataset/data.js R static/scripts/mvc/dataset/dataset-choice.js R static/scripts/mvc/dataset/dataset-edit-attributes.js R static/scripts/mvc/dataset/dataset-error.js R static/scripts/mvc/dataset/dataset-li-edit.js R static/scripts/mvc/dataset/dataset-li.js R static/scripts/mvc/dataset/dataset-list.js R static/scripts/mvc/dataset/dataset-model.js R static/scripts/mvc/dataset/states.js R static/scripts/mvc/form/form-data.js R static/scripts/mvc/form/form-input.js R static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-repeat.js R static/scripts/mvc/form/form-section.js R static/scripts/mvc/form/form-view.js R static/scripts/mvc/form/form-wrapper.js R static/scripts/mvc/grid/grid-model.js R static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/grid/grid-template.js R static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/history/copy-dialog.js R static/scripts/mvc/history/hda-li-edit.js R static/scripts/mvc/history/hda-li.js R static/scripts/mvc/history/hda-model.js R static/scripts/mvc/history/hdca-li-edit.js R static/scripts/mvc/history/hdca-li.js R static/scripts/mvc/history/hdca-model.js R static/scripts/mvc/history/history-content-model.js R static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-item-li.js R static/scripts/mvc/history/history-list.js R static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-preferences.js R static/scripts/mvc/history/history-structure-view.js R static/scripts/mvc/history/history-view-annotated.js R static/scripts/mvc/history/history-view-edit-current.js R static/scripts/mvc/history/history-view-edit.js R static/scripts/mvc/history/history-view.js R static/scripts/mvc/history/job-dag.js R static/scripts/mvc/history/job-states-model.js R static/scripts/mvc/history/multi-panel.js R static/scripts/mvc/history/options-menu.js R static/scripts/mvc/job/job-li.js R static/scripts/mvc/job/job-model.js R static/scripts/mvc/job/job-params.js R static/scripts/mvc/lazy/lazy-limited.js R static/scripts/mvc/library/library-dataset-view.js R static/scripts/mvc/library/library-folder-view.js R static/scripts/mvc/library/library-folderlist-view.js R static/scripts/mvc/library/library-folderrow-view.js R static/scripts/mvc/library/library-foldertoolbar-view.js R static/scripts/mvc/library/library-library-view.js R static/scripts/mvc/library/library-librarylist-view.js R static/scripts/mvc/library/library-libraryrow-view.js R static/scripts/mvc/library/library-librarytoolbar-view.js R static/scripts/mvc/library/library-model.js R static/scripts/mvc/library/library-util.js R static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-view.js R static/scripts/mvc/tag.js R static/scripts/mvc/tool/tool-form-base.js R static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tools.js R static/scripts/mvc/toolshed/categories-view.js R static/scripts/mvc/toolshed/repo-queue-view.js R static/scripts/mvc/toolshed/repo-status-view.js R static/scripts/mvc/toolshed/repositories-view.js R static/scripts/mvc/toolshed/repository-queue-view.js R static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/toolshed-model.js R static/scripts/mvc/toolshed/util.js R static/scripts/mvc/toolshed/workflows-view.js R static/scripts/mvc/tours.js R static/scripts/mvc/ui/error-modal.js R static/scripts/mvc/ui/icon-button.js R static/scripts/mvc/ui/popup-menu.js R static/scripts/mvc/ui/ui-buttons.js R static/scripts/mvc/ui/ui-color-picker.js R static/scripts/mvc/ui/ui-drilldown.js R static/scripts/mvc/ui/ui-frames.js R static/scripts/mvc/ui/ui-list.js R static/scripts/mvc/ui/ui-misc.js R static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js Log Message: ----------- Remove static/scripts/* from the dev branch, add to .gitignore. These will be manually added back to release branches along with any other artifacts for distribution. This slight release-time burden will (per feedback from multiple developers) make it easier to manage changes to -dev. Commit: 29a1bf05e68a54c4fc9242e86ec5d27c8ac1db1a https://github.com/galaxyproject/galaxy/commit/29a1bf05e68a54c4fc9242e86ec5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M .gitignore Log Message: ----------- Remove redundant subdir rules. 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static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R 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static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #5434 from dannon/static_scripts_dev_removal Remove static/scripts/* from the dev branch, add to .gitignore. Compare: https://github.com/galaxyproject/galaxy/compare/3864a1763ffa...204bb0e8fdf5

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[galaxyproject/galaxy] 8e32e9: Implement more collection workflow post job action...
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e32e93d6d8e048cbc77cb94f7c97b5ae0cfc6d6 https://github.com/galaxyproject/galaxy/commit/8e32e93d6d8e048cbc77cb94f7c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Implement more collection workflow post job actions. Implement hide, delete, add tag, and remove tag for output collections and mapped over collections. Fixes https://github.com/galaxyproject/galaxy/issues/1680. Commit: 5aed347c3025ad061c572c6a2bbdf53a7626d3cc https://github.com/galaxyproject/galaxy/commit/5aed347c3025ad061c572c6a2bbd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #5418 from jmchilton/collection_pja [18.01] Implement more intuitive collection PJA Commit: 935b8c948cf4e47d1ea08fbe51332b7c6f15caa0 https://github.com/galaxyproject/galaxy/commit/935b8c948cf4e47d1ea08fbe5133… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Add --skip_flakey_fails flag to CI script for API tests xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551 and following comments. Commit: 1bd8c4fd26b6dbb2824922cbc7f24ab9e8929bfe https://github.com/galaxyproject/galaxy/commit/1bd8c4fd26b6dbb2824922cbc7f2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Merge pull request #5455 from jmchilton/backport_flakey [18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests Commit: 7bbc46658a77d74a2447095b61b28e6e4ca32e06 https://github.com/galaxyproject/galaxy/commit/7bbc46658a77d74a2447095b61b2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix setting job failure exception This can happen when the job's tool is unavailble and outputs_to_working_directory is activated. Fixes https://github.com/galaxyproject/galaxy/issues/5424. Commit: f99299f8332a75a6075f49176770078be9cda571 https://github.com/galaxyproject/galaxy/commit/f99299f8332a75a6075f49176770… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Pre-compute more collection state during mapping. Still dealing with fallout from 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping. Commit: 51e030f4f3b608710adbba9ed4647db3d20196cb https://github.com/galaxyproject/galaxy/commit/51e030f4f3b608710adbba9ed464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bring in @mvdbeek's test cases from #5431. Commit: b2e8d891b7ca7e24aaf86b6e559356e7d62f3373 https://github.com/galaxyproject/galaxy/commit/b2e8d891b7ca7e24aaf86b6e5593… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable Fix setting job failure exception Commit: 207f5faba0ab70747c70de2d8d66a16ee2b00ecb https://github.com/galaxyproject/galaxy/commit/207f5faba0ab70747c70de2d8d66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5449 from jmchilton/collection_mapping_fixes [18.01] Collection mapping fixes for regression in 18.01. Commit: 3864a1763ffa101384314090066c671bca5ba23d https://github.com/galaxyproject/galaxy/commit/3864a1763ffa101384314090066c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f8d21f098af2...3864a1763ffa

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[galaxyproject/galaxy] f99299: Pre-compute more collection state during mapping.
by GitHub 04 Feb '18

04 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: f99299f8332a75a6075f49176770078be9cda571 https://github.com/galaxyproject/galaxy/commit/f99299f8332a75a6075f49176770… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Pre-compute more collection state during mapping. Still dealing with fallout from 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping. Commit: 51e030f4f3b608710adbba9ed4647db3d20196cb https://github.com/galaxyproject/galaxy/commit/51e030f4f3b608710adbba9ed464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bring in @mvdbeek's test cases from #5431. Commit: 207f5faba0ab70747c70de2d8d66a16ee2b00ecb https://github.com/galaxyproject/galaxy/commit/207f5faba0ab70747c70de2d8d66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5449 from jmchilton/collection_mapping_fixes [18.01] Collection mapping fixes for regression in 18.01. Compare: https://github.com/galaxyproject/galaxy/compare/b2e8d891b7ca...207f5faba0ab

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